[BioC] about plot rglist

[Jenny Drnevich]

See ?plotMA3by2  - I use it quite often, because it makes MA plots of all 
your arrays all on the same scale, puts 6 per page, and downloads the 
resulting files into your working directory.

Cheers,
Jenny

At 08:33 AM 9/12/2006, James W. MacDonald wrote:
>Hi Yanju,
>
>Please don't send questions directly to me. Using the BioC list is
>preferred for at least two reasons. First, there are many people on the
>BioC list who might have a better answer for your question. Second, the
>list is archived and available for people to search, and your question
>and any resulting answer may help someone in the future.
>
>yanju wrote:
> > Dear James,
> >
> > In analyse of DNA microarray using LIMMA, for example:
> > targets<-readTargets("target.txt")
> > rg<-read.maimages(targets$FileName,source="genepix",wt.fun=wtflags(0.1))
> >
> > when I plot rg by using:
> > plotMA(rg)
> > Only one array has been plotted, but actually, I have 8 arrays . I tried
> > plotMA(rg, array=8), it did not work neither.
> > I want to know how to plot MA imagin of multiple arrays.
> > Expectin your reply. Thank you in advance.
>
>As far as I know, plotMA() is only designed to plot one array at a time.
>If you want to plot all the arrays, you have several choices.
>
>1.) Plot all together in one window
>
>layout(matrix(1:8, nc = 2, byrow = TRUE))
>for(i in 1:8) plotMA(rg, array = i)
>
>2.) Make individual plots and save in a pdf
>
>pdf("MAplots.pdf")
>for(i in 1:8) plotMA(rg, array = i)
>dev.off()
>
>3.) If on Windows (you don't mention OS)
>
>windows(record = TRUE)
>for(i in 1:8) plotMA(rg, array = i)
>
>Then use Page up and Page down keys to cycle through windows.
>
>HTH,
>
>Jim
>
>
> >
> > Regards,
> > Yanju
>
>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>734-647-5623
>
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu